Restriction enzymes are endonucleases (see Glossary of Terms) which cleave DNA at short, specific nucleotide sequences. Purified DNA can be cleaved at these specific sites on the molecule and the length of the cleavage products measured. By a variety of experimental techniques, the order of these fragments in the molecule can be determined and thus one can "map" the restriction sites of a genome. At minimum, a map is an ordered list of restriction sites and their positions on the DNA molecule. A map may also contain an identification of every fragment in the data set as belonging to an interval on the map. For most purposes, the usefulness of a map is dependent on this information. Such a map is a physical map of the genome and can be correlated with a genetic map or with physical maps derived by other means (such as EM Heteroduplex analysis).
Restriction enzymes have proven useful for the physical dissection of the genomes of organisms ranging from bacteria to mammals. These endonucleases have been used to map and compare genomes, to produce DNA fragments for DNA sequencing and to construct recombinant DNA molecules. Maps are useful both for the isolation of defined regions of the genome and in the analysis of hybrid chromosomes and deletion mutants.
For example, restriction enzymes are the "scissors" used to cut large genomes (billions of nucleotides (bases) long) into pieces for subsequent molecular cloning. It was only the discovery of restriction enzymes and their characteristics which allowed the development of the analysis techniques collectively known as "recombinant DNA technology". The ability to clone pieces of DNA of interest out of the huge background of the genome and replicate them along with the cloning vector permits the isolation of useful amounts of reasonably pure DNA for study. This has led to experiments for the elucidation of molecular genetic details about gene structure and function that were impossible a decade ago.
Restriction enzymes are also an important tool of genome analysis. For example, when screening a "shotgun" (large, mixed collection of all clones of a genome) for a particular feature of interest, an experimenter generally finds a number of positive candidates. The relationship of the candidates can be elucidated by restriction mapping. Two candidates might be identical (and would thus have an identical restriction map), they might be overlapping (and would thus each have a part of its map identical with the other) or they might be unrelated (and would thus have quite different restriction maps). In the case of overlapping clones, this kind of analysis further locates the feature selected for when isolating the positive candidates to the DNA contained in both clones (i.e., the overlapping region of the restriction maps). If two of the candidates selected have unrelated maps, this suggests that two different regions of the genome (two different "genes") can produce the same feature selected for.
Similarly, genomes related in a number of ways can be compared by their restriction maps. For example, two related but distinct organisms (such as bacteriophage lambda and bacteriophage phi 80) can genetically recombine to yield recombinent progeny with some of the features of each parent. If one determines a restriction map of the recombinant and compares it with the maps of the parents, one can determine which region of the genome came from which parent, where the recombination events occured in the DNA, and may be able to assign some of the features to particular regions in the DNA.
In recent years it has become possible to determine the nucleotide sequence of DNA in a particular gene or region of interest. DNA is a linear string of subunits, each subunit can be one of four types (A,G,C, or T). The experiments to determine the sequence or order of subunits in a given region of DNA are greatly facilitated by having a restriction map of the region of interest.